Use of mRNA-seq data to select Malus x domestica (apple) genes for use as quantitative PCR reference genes

The selection of reference genes for RT-qPCR requires the measurement of gene expression across experimental samples. A reference gene with a low variance in its expression for one set of samples may not be suitable for other experiments sampled across different developmental stages, tissue types and seasons. The latter are often typical of postharvest gene expression experiments. In this study we initially used 61 mRNA-seq data sets from different tissues, stages of development and stress conditions of apple (Malus x domestica) to select 10 potential reference genes. These were tested using RT-qPCR, reference gene selection software, and 156 mRNA-seq datasets from a second independent laboratory. From these results we have selected four potential reference genes for use in postharvest and other apple gene expression experiments. Use of this mRNA-seq data method may facilitate selection of reference genes in other crop species for which these data are available.